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The real answer, as currently understood by science, has to do with Vitamin D.
Humans evolved in Africa over millions of years, and originally we were all black. Evolution pushed black skin in humans (as with other hairless mammals) as a protection against cellular UV damage. An originally unrelated evolutionary detail was the fact that humans require vitamin D, and that we manufacture vitamin D in our skin when we're exposed to sunlight.
When humans moved out of Africa, we moved to places with less natural sunlight than we'd evolved to deal with, and we began covering ourselves with animal skins to ward off the colder climates we were moving into. The sudden reduction in sunlight making it to the skin reduced vitamin D generation, damaging health and reducing reproductive success. The result? Human skin, outside of Africa, began to lighten. Lighter skin allows more sunlight through, which increases vitamin D generation. The further north you went, the lighter you got (before you bring them up, the Inuit are an exception because of their vitamin D heavy seafood diets). This process took, by some estimates, about 50,000 years to complete.
The ancient ancestors of the Native Americans, including those who live in Central America, originated from what is today Siberia, Mongolia, and other parts of eastern Asia between 35,000 and 15,000 years ago. None of them (or too few to matter) came directly from Africa, so none were black. None (or too few to matter) were from northwestern Asia, so none were white. Virtually all came from that "brown" middle, so those were the only genes that carried foreward.
When the first natives moved into Central America, they found a heavily forested region where sunlight reached the surface only in limited areas, or not at all. Because sunlight wasn't unlimited, there was no evolutionary push to darken the skin again. Even if there was, population migrations over time haven't yet given evolution the opportunity to darken them up. If you deforested Guatamala, prevented anyone else from moving in, limited the amount of clothes they could wear, and then checked back in 50,000 years, you'd find a bunch of black Guatamalans.
And that's why Central American's aren't black. Evolution.
This is also why it's important to learn the answers to questions like "Why are some people gay?" Answering seemingly trivial questions like that can often open up huge windows onto our history and evolutionary past. They teach us things about ourselves that can change our perspectives on mankind as a whole.
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